Description Usage Arguments Value Examples
This is an important internal function to calculate distance matrix, it is used particularly in Tree.build.2nd.treemaking
1 2 3 4 5 6 | dist.matrix.prep.v3(binary.primary, datainfo.col1 = c("res.0.6", "nUMI",
"Sample"), datainfo.col2 = c("res.0.6", "nUMI", "Sample"),
datainfo.col.dog = c("res.0.6", "nUMI", "Sample"),
cluster.col1 = "res.0.6", cluster.col2 = "res.0.6",
cluster.col.dog = "res.0.6", withsingledog = F,
dog.seurat.ob = NULL, neighborwithdog.seurat.ob = NULL)
|
binary.primary |
This is the primary clustering result that can be retrieved from Tree.build.prepare object. (Because Tree.build.prepare mainly do the primary clustering.)The input here is tree.prep.ob$primary.total |
datainfo.col1 |
default is c("res.0.6","nUMI","Sample") |
datainfo.col2 |
default is c("res.0.6","nUMI","Sample") |
datainfo.col.dog |
c("res.0.6","nUMI","Sample") |
cluster.col1 |
default is "res.0.6" |
cluster.col2 |
default is "res.0.6" |
cluster.col.dog |
"res.0.6" |
withsingledog |
Default is F |
dog.seurat.ob |
=NULL |
neighborwithdog.seurat.ob |
=NULL |
This will return an object used for Tree.build.2nd.treemaking
1 | total.dist.matrxes<-dist.matrix.prep(primary.total,datainfo.col1=c(paste("res.",first.reso[1],sep=""),"nUMI","Sample"),cluster.col1=paste("res.",first.reso[1],sep=""),datainfo.col2=c(paste("res.",first.reso[2],sep=""),"nUMI","Sample"),cluster.col2=paste("res.",first.reso[2],sep=""),res1=paste("res.",first.reso[1],sep=""),res2=paste("res.",first.reso[2],sep=""))
|
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